Nir Hacohen

Massachusetts General Hospital
Ctr. for Immunology and Inflammatory Diseases
149 13th Street, Bldg.149, Rm. 8410
Charlestown, MA 02129

Broad Institute
7 Cambridge Center
Cambridge, MA 02142

Tel: 617-724-3768
Fax: 617-726-5651
Lab Members: 5 Postdoctoral Fellows, 7 Graduate Students
Visit my lab page here and here.

The Hacohen lab uses systems-wide genetic and biochemical approaches to describe the mechanisms underlying specificity in pathogen-sensing pathways, the interactions of pathogens with their hosts and the initiation of autoimmunity. The major projects in the lab focus on how: (1) TLRs and other pathogen sensors achieve specificity in their induction of gene expression; (2) influenza virus modulates host responses; (3) to develop systematic methods to reconstruct signaling and transcriptional networks.

Pathogen-sensing by the innate immune system. The immune system can normally distinguish and respond appropriately to a broad diversity of pathogens and antigens that it encounters during a lifetime – including the products of bacteria, fungi, viruses and mammalian cells. Dendritic cells (DCs) play an important role in this process through their highly developed machinery to sense and engulf pathogens and to process and present digested peptides to T cells. We had previously shown that dendritic cells exhibit unique gene expression signatures, including specific cytokine, chemokine and costimulator expression, in response to distinct pathogens. Our current studies focus on revealing the genetic networks underlying innate immune responses and host-pathogen interactions. We are interested in addressing the following kinds of questions: (1) What are the mechanisms by which each innate sensor induces specific cellular responses? (2) What is the role of innate sensory pathways in the induction of protective immunity to infections and tumors? (3) How are these pathways dysregulated under some conditions, leading to inflammatory disorders or autoimmune disease? (4) How do pathogens manipulate the host response, and how does innate immune activation shift the balance to protect the host? To address these questions, we utilize genetic, biochemical and cell biological approaches to systematically dissect the genetic circuitry of pathogen-sensing pathways and their role in initiating and guiding immune responses.

RNAi library for loss-of-function genetics in mammalian cells. Genetic screening in lower organisms has been the basis of critical discoveries across many fields. To develop a method for systematic genetic screens in mammals, we have (as part of a consortium with the Sabatini and Hahn labs, and under the direction of David Root at the Broad Institute): (a) generated genome-wide lentiviral shRNA libraries targeting human and mouse genes at the Broad Institute (Moffat et al., 2006; Luo et al., 2008); (b) developed high-throughput protocols to generate viral particles and infect cells in order to enable large-scale loss-of-function screens in mammalian cells; (c) demonstrated that these viruses can infect primary dendritic cells (and many other immune and non-immune cell types) and silence genes that control DC functions (Amit et al., 2009; Chevrier et al., 2011). As the Broad Institute RNAi Consortium and Platform continues to refine this technology and develop applications to many biological systems, we have begun to apply this powerful methodology to dissect the circuitry of the immune system (Oberdoerffer et al., 2008; Amit et al., 2009; Shapira et al., 2009; Chevrier et al., 2011). We are currently focused on adapting the libraries for in vivo RNAi screens and studies.

What are the genes that control dendritic cell maturation and antigen presentation in response to microbes and their products? Dendritic cells exhibit an ordered cascade of processes during maturation including: pathogen recognition, engulfment and destruction; antigen processing and presentation; cytokine, chemokine and costimulator production; migration to draining lymph nodes; and finally, CD4 and CD8 T cell engagement. How are these processes regulated by TLR and other pathogen sensors upon exposure of DCs to microbes or their products? What are the pathway branchpoints that confer specificity of output? How are these pathways self-limiting? To enable the identification of genes and pathways required in these processes, we have use the lentiviral RNAi library to infect primary mouse bone marrow-derived DCs, and then assayed the effects of gene perturbation on several cell biological outputs. Ongoing projects use this approach to identify and study critical genes of innate immunity. We have been developing a systems biology strategy (in collaboration with Aviv Regev’s group) in which we discovered and characterized a set of transcription and chromatin factors (Amit et al., 2009) and signaling molecules (Chevrier et al., 2011) that mediate TLR responses. Finally, we are extending our approach to humans with the goal of determining immune network function and structure in individuals during health and disease.

How do vesicle trafficking events contribute to the ability of activated macrophages to restrict intracellular bacteria? Vacuolar pathogens (such as Legionella and Mycobacterium tuberculosis) are able to set up a replicative niche in the hostile environment of the mouse and human macrophage phagosome by resisting phagosome maturation. In macrophages activated by interferon gamma (IFNγ), though, the equilibrium tips in the favor of phagosome maturation, bacterial restriction, and macrophage survival. Our goal is to link specific vesicle trafficking events to targeting of the bacterial phagosome by lysosomes, autophagy-related proteins, or other entities involved in phagosome maturation.

What are the host factors involved in detection and replication of RNA viruses? While most viral genomes encode for proteins that mediate viral entry, replication and assembly, viruses are still dependent on host factors for their life cycle within cells. The genome of RNA viruses, for example, is synthesized, processed, transported and packaged within a host cell. For many of these processes, the identity and function of the host factors are not known. In addition, RNA viruses are detected by a system of RNA sensors that trigger host defenses. Our focus is on the segmented negative-stranded influenza A virus and identifying identify host factors that confer susceptibility or resistance to influenza infection in primary human lung epithelial cells. In particular, we have developed another systems approach that combines transcriptional profiling, yeast-2-hybrid analysis and RNAi to comprehensively identify functional host gene products that play a role in: (1) innate immune sensing of viral RNA and influenza virus and (2) the life cycle of influenza (Shapira et al., 2009). In addition, we are performing detailed studies of novel restriction factors and immune modulators

Chevrier N, Mertins P, Artyomov MN, Shalek AK, Iannacone M, Ciaccio MF, Gat-Viks I, Tonti E, DeGrace MM, Clauser KR, Garber M, Eisenhaure TM, Yosef N, Robinson J, Sutton A, Andersen M, Root DE , von Andrian U, Jones RB, Park H, Carr SA, Regev A*, Amit,I*, Hacohen N*. Systematic Discovery of Signaling Components Identifies New Branches in Viral-Sensing Pathways. Cell 2011, 147: 853-867

Amit I, Regev A, Hacohen N. Strategies to discover regulatory circuits of the mammalian immune system. Nat Rev Immunol. 2011 Nov 18;11(12):873-80.

Pe’er D, Hacohen N. Principles and Strategies for Developing Network Models in Cancer. Cell, 2011. 144(6):864-73.

Shapira SD, Hacohen N. Systems biology approaches to dissect mammalian innate immunity. Curr Opin Immunol. 2010, 23:71-77.

Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N*, Regev A*. Unbiased reconstruction of a mammalian transcriptional network mediating the differential response to pathogens. Science. 2009 Oct 9;326:257-63.

Shapira S, Gat-Viks I, Shum BOV, Dricot A, Degrace MM, Wu L, Gupta PB, Hao T, Silver SJ, Root DE, Hill DE, Regev A*, Hacohen N*. A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell, 2009, Dec 24; 139:1255-1267.

Oberdoerffer S, Moita LF, Neems D, Freitas RP, Hacohen N, Rao A. Regulation of CD45 alternative splicing by heterogeneous ribonucleoprotein, hnRNPLL. Science. 2008 321:686-91.

Luo B, Cheung HW, Subramanian A, Sharifnia T, Okamoto M, Yang X, Hinkle G, Boehm JS, Beroukhim R, Weir B, Mermel C , Barbie C, Awad T, Zhou X, Nguyen T, Piqani B, Li C, Golub TR, Meyerson M, Hacohen N*, Hahn WC*, Lander ES*, Sabatini DM*, Root DE*. Highly parallel identification of essential genes in cancer cells. PNAS 2008, 105:20380-5.

Moffat J, Grueneberg D, Yang X, Kim SY, Kloepfer AM, Hinkle G, Piqani B, Eisenhaure TM, Luo B, Grenier JK, Carpenter AE, Foo SY, Stewart SA, Stockwell BR, Hacohen N*, Hahn WC*, Lander ES*, Sabatini DM*, Root DE*. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell. 2006; 124:1283-98

(*Equal contributors)

Last Update: 1/6/2014